GATK4: Fix joint calling issue with MMQ, MCL
GATK4: Fix joint calling issue with MMQ, MCL

The VCF headers for GATK4 beta3 outputs have incorrect representations
for MMQ, MCL. This causes truncation of inputs to GenomicsDB, resulting
in missing calls during joint gVCF calling. This works around the issue
by fixing the VCF headers during gVCF region merging.

https://github.com/broadinstitute/gatk/issues/3429#issuecomment-324188028

biocyberman/bcbio-nextgen,biocyberman/bcbio-nextgen,lbeltrame/bcbio-nextgen,a113n/bcbio-nextgen,chapmanb/bcbio-nextgen,chapmanb/bcbio-nextgen,lbeltrame/bcbio-nextgen,chapmanb/bcbio-nextgen,lbeltrame/bcbio-nextgen,vladsaveliev/bcbio-nextgen,biocyberman/bcbio-nextgen,vladsaveliev/bcbio-nextgen,vladsaveliev/bcbio-nextgen,a113n/bcbio-nextgen,a113n/bcbio-nextgen